#============================================================*
#            test simulation of cylinders from domain        *
#                                                            *
# allign cylinders with previous one.                        *
#============================================================*

# set units
#----------
units
units scale  name = mass   uname = reducedMass   value = 10000.0


# open pdb file
#--------------
database open name =  neck_xform  format = pdb file =  ../../data/neck_xform.pdb

# read molecule
#--------------
molecule read  database =  neck_xform  name = m1  model = 1  type = protein

# create domains 
#---------------
domain create hc = C
# translate domain so that ground joint will be (0,0,0)
domain hc  xform translation = [ 0.15334 -0.208601 -0.332707 ]
domain hc  backbone  color = [ 0.6 0.6 0.6 ] width = 1 show

# create cylinder
#----------------
solid create  name = cyl1  type = cylinder  \
              radius = 0.22                 \
              domain = hc                   \
              region = C[762-780]           \
              atoms = { CA }                \
              color = [ 1 0 0 ]             \
              display = line                \
              show = true

# create cylinder
#----------------
solid create  name = cyl2  type = cylinder  \
              radius = 0.22                 \
              domain = hc                   \
              region = C[780-796]           \
              atoms = { CA }                \
              allign = cyl1                 \
              color = [ 0 1 0 ]             \
              display = line                \
              show = true

# create cylinder
#----------------
solid create  name = cyl3  type = cylinder  \
              radius = 0.22                 \
              domain = hc                   \
              region = C[796-814]           \
              atoms = { CA }                \
              allign = cyl2                 \
              color = [ 1 1 0 ]             \
              display = line                \
              show = true

# create cylinder
#----------------
solid create  name = cyl4  type = cylinder  \
              radius = 0.22                 \
              domain = hc                   \
              region = C[814-832]           \
              atoms = { CA }                \
              allign = cyl3                 \
              color = [ 0 1 1 ]             \
              display = line                \
              show = true

# create bodies                           
#--------------
body create  name = ground    type = ground
body create  name = cyl1_body type = rigid  solid = cyl1
body create  name = cyl2_body type = rigid  solid = cyl2
body create  name = cyl3_body type = rigid  solid = cyl3
body create  name = cyl4_body type = rigid  solid = cyl4


# create joints
#--------------

joint create  name = jnt1  type = ball  cylinder = cyl1  distance = 0.0
joint jnt1 color = [ 1 1 1 ] msize = 0.1 shading = color show = true
joint jnt1 bodies = { ground cyl1_body }

joint create  name = jnt2  type = ball cylinder = cyl1  distance = 1.0 
joint jnt2 color = [ 1 0 0 ] msize = 0.1 shading = color show = true
joint jnt2 bodies = { cyl1_body cyl2_body }

joint create  name = jnt3  type = ball cylinder = cyl2  distance = 1.0 
joint jnt3 color = [ 0 1 0 ] msize = 0.1 shading = color show = true
joint jnt3 bodies = { cyl2_body cyl3_body }

joint create  name = jnt4  type = ball  cylinder = cyl3  distance = 1.0 
joint jnt4 color = [ 1 1 0 ] msize = 0.1 shading = color show = true
joint jnt4 bodies = { cyl3_body cyl4_body }


# create a rigid simulation  
#--------------------------

simulation create name = rsim  type = rigid

# set solver
#-----------
simulation rsim solver = ode
simulation rsim solver finite_rotation = on


# add bodies
#-----------
simulation rsim add body = ground
simulation rsim add body = cyl1_body
simulation rsim add body = cyl2_body
simulation rsim add body = cyl3_body
simulation rsim add body = cyl4_body

# add joints
#-----------
simulation rsim add joint = jnt1
simulation rsim add joint = jnt2
simulation rsim add joint = jnt3
simulation rsim add joint = jnt4

# add forces
#-----------
force create  name = force1           \
              type = explicit         \
              point = [ 0 0 0 ]       \
              direction = [ 1 0 0 ]   \
              scale = 1.0        

simulation rsim add force = force1    \
                    body = cyl4_body  \
                    time = { 0 1000 }

# initialize simulation
#----------------------
simulation rsim initialize

# step simulation
#----------------
simulation rsim step = 100